LAMMPS (18 Jul 2015)
# 250 butane system for drude polarizability example (Langevin)

units real
boundary p p p

atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
special_bonds lj/coul 0.0 0.0 0.5

pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0
pair_modify mix geometric tail yes
kspace_style pppm 1.0e-4

read_data data.butane
  orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1)
  2 by 1 by 2 MPI processor grid
  reading atoms ...
  4500 atoms
  scanning bonds ...
  5 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  9 = max dihedrals/atom
  reading bonds ...
  4250 bonds
  reading angles ...
  6000 angles
  reading dihedrals ...
  6750 dihedrals
  5 = max # of 1-2 neighbors
  8 = max # of 1-3 neighbors
  12 = max # of 1-4 neighbors
  17 = max # of special neighbors

comm_modify vel yes

group gBUTANE molecule 1:250
4500 atoms in group gBUTANE
group gCORES type 1 2 3
3500 atoms in group gCORES
group gDRUDES type 4 5
1000 atoms in group gDRUDES

pair_coeff    1    1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
pair_coeff    1    2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H
pair_coeff    1    3 lj/cut/coul/long 0.044496 2.958040 # C3H H
pair_coeff    2    2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H
pair_coeff    2    3 lj/cut/coul/long 0.044496 2.958040 # C2H H
pair_coeff    3    3 lj/cut/coul/long 0.029999 2.500000 # H H
pair_coeff    *  4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
pair_coeff    1    * thole 1.368000
pair_coeff    2    * thole 1.368000
pair_coeff    4    * thole 1.368000
pair_coeff    5    * thole 1.368000

neighbor 2.0 bin

variable vTEMP   equal 260.0
variable vTEMP_D equal 1.0
variable vPRESS  equal 1.0

velocity gCORES  create ${vTEMP} 12345
velocity gCORES  create 260 12345
velocity gDRUDES create ${vTEMP_D} 12345
velocity gDRUDES create 1 12345

fix fDRUDE all drude C C N D D

fix fSHAKE gCORES shake 0.0001 20 0 b 2 4
  0 = # of size 2 clusters
  500 = # of size 3 clusters
  500 = # of size 4 clusters
  0 = # of frozen angles

fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes
fix fNPH all nve

compute cTEMP all temp/drude

thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
thermo 50

timestep 0.5
run 2000
PPPM initialization ...
  G vector (1/distance) = 0.367867
  grid = 36 36 36
  stencil order = 5
  estimated absolute RMS force accuracy = 0.031354
  estimated relative force accuracy = 9.44215e-05
  using double precision FFTs
  3d grid and FFT values/proc = 26875 11664
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 17
New max number of 1-2 to 1-4 neighbors: 17 (+0)
Neighbor list info ...
  2 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  master list distance cutoff = 10
  ghost atom cutoff = 10
Memory usage per processor = 14.7792 Mbytes
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume cTEMP[1] cTEMP[2] 
       0            0    6535.5187      2714.74    248.45112    3820.7787    3724.3278    140.75328    1.4735401            0   -518.77975    595169.42   -594696.41    -353319.1    55742.797    334.61375    18.435655 
      50   0.91017509    3449.6475    2040.7698    186.76984    1408.8777    836.85155    816.32124    115.24642            0    -758.7276    595242.44   -594843.26    3042.2937    55742.797    199.51659     152.7045 
     100     1.829694    2917.9137     1947.102    178.19743    970.81176    363.96553    932.94225    165.60761            0   -931.00296    595306.34   -594867.04    1697.0127    55742.797    226.24749    49.885738 
     150    2.6620312    2853.3142    1959.0731    179.29301    894.24108    244.19792    978.17893    187.28366            0   -941.03478    595295.44   -594869.82    4597.2005    55742.797    241.05848    14.405808 
     200    3.4969041    2885.6715    1928.6381    176.50762    957.03347    227.09245    1066.5297     186.6858            0   -949.52603    595296.49   -594870.24    2602.8275    55742.797    240.70211    5.1458056 
     250     4.621171    2905.8961    1939.7876    177.52802    966.10847    215.77945    1122.1238    195.98218            0   -993.52132    595296.54   -594870.79    1808.1681    55742.797    243.04306     2.643716 
     300    5.5216351    2968.5517    1974.9277    180.74402      993.624    210.11413    1158.7871      194.142            0   -996.53154    595297.91   -594870.79    3371.8618    55742.797     247.7682    1.8321312 
     350    6.3789251     2996.151    1992.9982    182.39782    1003.1527    217.80518     1150.726    205.32316            0   -996.14478    595296.05   -594870.61    3022.9945    55742.797    250.15947    1.5176819 
     400     7.208317    2991.7201    1975.3852    180.78589    1016.3349    221.46133    1169.8254    213.90874            0   -1016.9906    595298.44   -594870.31    753.59124    55742.797    247.99744    1.3743032 
     450    8.0359671    3061.6051    2009.1302    183.87421    1052.4749    212.54169    1234.7697    205.71762            0   -1028.2259    595297.95   -594870.28    996.71341    55742.797    252.23801    1.3870863 
     500    8.8456361    3127.3783    2009.8033    183.93581    1117.5749    222.16507    1246.5854    215.82607            0   -994.66665     595298.3   -594870.63    2537.6157    55742.797    252.32947     1.367397 
     550    9.6647151     3181.037    2069.9836    189.44346    1111.0534    218.00575     1246.961    212.55852            0   -992.83597    595296.16   -594869.79    1333.8768    55742.797    259.86467    1.4641506 
     600    10.484356    3194.2009    2007.5349     183.7282     1186.666    228.93838    1309.4718    215.93595            0   -995.70641    595297.81   -594869.79    1336.7994    55742.797    252.00698    1.4677515 
     650     11.30116    3145.4387    2028.2544    185.62444    1117.1843    209.73722    1277.9793    217.12799            0   -1015.2398    595297.88    -594870.3    1442.6875    55742.797    254.61499    1.4639962 
     700    12.106719    3163.3345    2053.2645    187.91335      1110.07    209.45249    1257.3108     216.7541            0   -1000.1505    595296.63   -594869.92    1093.9724    55742.797    257.76091    1.4652884 
     750    12.924665    3145.6215    2010.7195    184.01966     1134.902    224.53065    1248.3301    222.25374            0    -988.4479    595298.83   -594870.59    470.73988    55742.797    252.39115    1.5116555 
     800    13.736913    3191.2614    2043.4195    187.01234     1147.842    225.71717    1239.3564    234.89539            0   -980.97352    595299.07   -594870.22    1472.0305    55742.797    256.53524    1.4309304 
     850    14.550736    3157.6279    2004.8472    183.48223    1152.7806    217.72587    1269.3398    224.40554            0   -987.51794    595299.15   -594870.32    293.76575    55742.797    251.69397    1.4007963 
     900    15.344895    3188.5027     2077.065    190.09155    1111.4377    216.92608    1251.4141     213.7672            0   -1000.1269     595299.5   -594870.05    702.56821    55742.797     260.7853    1.3847905 
     950    16.157597    3205.6761    2090.9807     191.3651    1114.6954     223.7729    1252.7887    225.91029            0   -1016.3682    595299.15   -594870.56   -19.492925    55742.797    262.50762    1.4603579 
    1000    16.969809    3231.5931    2078.7058    190.24172    1152.8873    228.77504    1273.1611    219.28923            0   -995.58473    595296.82   -594869.57    1292.4071    55742.797    260.98775    1.3954023 
    1050    17.771785    3264.2837    2106.0113     192.7407    1158.2724    224.16481    1278.5557    212.91309            0   -985.93386    595298.71   -594870.14    1357.1588    55742.797    264.40381    1.4463397 
    1100    18.572331    3243.3355    2125.1664    194.49376    1118.1691    227.38559    1247.5134    210.61488            0   -996.85878    595299.68   -594870.17    650.53225    55742.797    266.82195    1.4240918 
    1150     19.40463    3255.4144    2096.5982    191.87922    1158.8162    234.11389    1267.4257    217.02225            0   -989.70892    595299.81   -594869.84    688.78475    55742.797     263.2133    1.4631154 
    1200    20.321045    3266.2609    2088.3727    191.12642    1177.8882    225.40174    1284.1097    225.77008            0   -985.63518    595297.81   -594869.57    182.80287    55742.797    262.21901    1.3550749 
    1250    21.233994    3277.4365    2093.1481    191.56346    1184.2884    250.33569    1267.9985    235.70102            0   -999.80819    595299.96    -594869.9    780.87528    55742.797    262.80001    1.4077597 
    1300    22.113268    3280.4141    2121.4996    194.15818    1158.9145    228.23585    1259.7304    230.65174            0   -989.06345    595298.99   -594869.63    932.19341    55742.797    266.34543    1.4646736 
    1350    23.007421    3272.2214     2088.047    191.09662    1184.1744    224.66504     1284.656    217.03214            0    -970.5252    595297.72   -594869.37    63.097535    55742.797    262.16781    1.3823451 
    1400    23.903494    3239.3096    2099.1837    192.11584    1140.1259     221.3215    1252.8691    215.64014            0   -978.70393    595298.89   -594869.89    1125.3057    55742.797    263.59141    1.3221979 
    1450    24.833224     3226.293    2042.7354    186.94973    1183.5576    241.40449     1273.025    233.66813            0   -994.70934    595299.55   -594869.38   -412.31857    55742.797    256.45155    1.4245996 
    1500    25.736203    3245.4596    2097.0431    191.91994    1148.4164     250.3854    1248.1507    212.36871            0   -990.48467    595297.36   -594869.36    245.49743    55742.797    263.28349    1.4252034 
    1550    26.633033    3308.5518    2113.8467    193.45778    1194.7051     234.5293    1286.7563    233.20552            0   -987.36764    595297.06   -594869.48    1324.7098    55742.797    265.37419    1.4864431 
    1600    27.530123     3319.786    2130.8949    195.01803    1188.8911    234.06508    1292.3987    225.94876            0   -992.81161     595299.1   -594869.81    343.14209    55742.797    267.51024    1.5104547 
    1650     28.41116    3239.0425    2066.8485    189.15654     1172.194    219.46922    1303.0071    210.00869            0   -989.28577    595298.63   -594869.64   -505.97551    55742.797    259.48305    1.4300292 
    1700    29.313339    3281.3023     2054.581    188.03383    1226.7213    224.72686    1339.1948    208.65914            0   -974.24634    595297.79    -594869.4    331.11846    55742.797    257.92342    1.4735531 
    1750    30.216241    3237.8348    2043.3835    187.00904    1194.4513    238.16066    1281.9383    221.74494            0   -976.72731     595299.4   -594870.06    612.69867    55742.797    256.53793    1.4116726 
    1800    31.113153    3242.1274      2087.94    191.08683    1154.1873    240.53142    1256.6966    210.49591            0   -983.16111    595299.34   -594869.72   -8.1277769    55742.797    262.14149    1.4166426 
    1850    31.993161    3249.8016    2079.8947    190.35052    1169.9069    233.21641    1269.4077    215.23716            0   -975.12835     595296.5   -594869.33    1156.1724    55742.797    261.13101    1.4122227 
    1900    32.891621    3251.9579    2097.6037    191.97124    1154.3541    243.13703    1228.3357    235.37914            0   -983.06313    595300.37    -594869.8    293.60486    55742.797    263.33664    1.4715416 
    1950    33.791255    3202.0703    2076.0894    190.00227    1125.9809    233.71337    1217.6976    227.58496            0    -981.8352    595298.07   -594869.25   -544.65606    55742.797    260.61868    1.5018224 
    2000    34.690323    3215.7987    2015.5993    184.46625    1200.1994    242.43605    1281.6846    227.48326            0   -980.70325    595298.82   -594869.52    248.82508    55742.797    253.04055    1.4169879 
Loop time of 34.6904 on 4 procs for 2000 steps with 4500 atoms

Pair  time (%) = 16.514 (47.6038)
Bond  time (%) = 4.35555 (12.5555)
Kspce time (%) = 10.6198 (30.613)
Neigh time (%) = 0.393407 (1.13405)
Comm  time (%) = 1.18699 (3.42165)
Outpt time (%) = 0.00467861 (0.0134867)
Other time (%) = 1.6161 (4.65863)

Nlocal:    1125 ave 1219 max 1009 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Nghost:    5768 ave 5890 max 5664 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Neighs:    215002 ave 223956 max 206872 min
Histogram: 2 0 0 0 0 0 0 0 1 1

Total # of neighbors = 860008
Ave neighs/atom = 191.113
Ave special neighs/atom = 13.3333
Neighbor list builds = 29
Dangerous builds = 0
